Abstract
The expression of distorted DNA-binding factors was studied in developing zebrafish (Danio rerio) using UV-damaged DNA as the binding target. A strong and high-shifting binding activity was detected in the extracts of zebrafish early embryos (12 h after fertilization), and the expression of this activity dramatically decreased in 60 to 84-h-old zebrafish. The embryonic extracts produced a similar pattern of high-shifting complexes after incubating with a CPD-specific or a 6-4PP-specific probe, while different types of low-shifting complexes were generated by the extracts of 84-h-old larvae. The formation of high-shifting complexes was suppressed in the presence of NaCl at 0.25 M or higher concentrations, yet the production of low-shifting complexes was stimulated by increasing salt concentration. The binding activity expressed in zebrafish embryos was apparently unrelated to NER-associated damage-recognition protein XPA, since two polypeptides recognized by an anti-human XPA antibody were detected only in 84-h-old zebrafish extracts. A competitive binding assay indicated that both CPDs and 6-4PPs were recognized by the same binding activity expressed in 12-h-old zebrafish, and this activity contained at least two protein fractions that were eluted from a DEAE-cellulose column by NaCl at 0.1 M and 0.2 M. UV crosslinking of the two NaCl eluates to a 6-4PP probe produced covalent complexes with the same electrophoretic mobility except one 34-kDa complex generated by the 0.1 M NaCl eluate, suggesting the existence of two multisubunit damage-recognition protein complexes in zebrafish embryos. UV-binding factors found in 12-h-old zebrafish embryos may be involved in processing developmental stage-specific DNA structures similar to UV-damaged DNA.
Similar content being viewed by others
References
Abramic, M., Levine, A.S. and Protic, M. 1991. Purification of an ultraviolet-inducible, damage-specific DNA-binding protein from primate cells. J. Biol. Chem. 266: 22493–22500.
Bradford, M.M. 1976. A rapid and sensitive method for quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248–254.
Brownile, A. and Zon, L. 1999. The zebrafish as a model system for the study of hematopoiesis. Bioscience 49: 382–392.
Burns, J.L., Guzder, S.N., Sung, P., Prakash, S. and Prakash, L. 1996. An affinity of human replication protein A for ultravioletdamaged DNA: Implications for damage recognition in nucleotide excision repair. J. Biol. Chem. 271: 11607–11610.
Chan, G.L., Doetsch, P.W. and Haseltine, W.A. 1985. Cyclobutane pyrimidine dimers and (6-4)photoproducts block polymerization by DNA polymerase I. Biochemistry 24: 5723–5728.
Cleaver, J.E. and States, J.C. 1997. The DNA damage-recognition problem in human and other eukaryotic cells: The XPA damage binding protein. Biochem. J. 328: 1–12.
Cleaver, J.E., Charles, W.C., McDowell, M.L., Sadinski, W.J. and Mitchell, D.L. 1995. Overexpression of the XPA repair gene increases resistance to ultraviolet radiation in human cells by selective repair of DNA damage. Cancer Res. 55: 6152–6160.
Driever, W., Stemple, D., Schier, A. and Solnica-Krezel, L. 1994. Zebrafish: genetic tools for studying vertebrate development, Trends Genet. 10: 152–159.
Franklin, W.A., Doetsch, P.W. and Haseltine, W.A. 1985. Structural determination of the ultraviolet light-induced thymine-cytosine pyrimidine-pyrimidone(6-4) photoproduct. Nucl. Acids Res. 13: 5317–5325.
He, Z., Henricksen, L.A., Wold, M.S. and Ingles, C.J. 1995. RPA involvement in the damage-recognition and incision steps of nucleotide excision repair. Nature 374: 566–569.
Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K. and Shirakawa, M. 1999. Resonance assignments, solution structure, and backbone dynamics of the DNA-and RPA-binding domain of human repair factor XPA. J. Biochem. 125: 495–506.
Jones, C.J. and Wood, R.D. 1993. Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32: 12096–12104.
Keeney, S., Chang, G.I. and Linn, S. 1993. Characterization of a human DNA damage binding protein implicated in xeroderma pigmentosum E. J. Biol. Chem. 268: 293–300.
Kim, S.T., Malhorta, K., Taylor, J.S. and Sancar, A. 1996. Purification and partial characterization of (6-4)photoproduct photolyase from Xenopus laevis. Photochem. Photobiol. 63: 292–295.
Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B. and Schilling, T.F. 1995. Stages of embryonic development of the zebrafish. Dev. Dyn. 203: 253–310.
Kubota, S., Ishibashi, T. and Kohno, S. 1997. A germline restricted highly repetitive DNA sequence in Paramyxine atami: An interspecifically conserved, but somatically eliminated, element. Mol. Gen. Genet. 256: 252–256.
Lippke, J.A., Gordon, L.K., Brash, D.E. and Haseltine, W.A. 1981. Distribution of UV light-induced damage in a defined sequence of human DNA: Detection of alkaline-sensitive lesions at pyrimidine nucleoside-cytidine sequences. Proc. Natl. Acad. Sci. USA 78: 3388–3392.
Mitchell, D.L. and Nairn, R.S. 1989. The biology of the (6-4) photoproduct. Photochem. Photobiol. 49: 805–819.
Otoshi, E., Yagi, T., Mori, T., Matsunaga, T., Nikaido, O., Kim, S.T., Hitomi, K., Ikenaga, M. and Todo, T. 2000. Respective roles of cyclobutane pyrimidine dimers, (6-4) photoproducts, and minor photoproducts in ultraviolet mutagenesis of repair-deficient xeroderma pigmentosum A cells. Cancer Res. 60: 1729–1735.
Otrin, V.R., McLenigan, M., Takao, M., Levine, A.S. and Protic, M. 1997. Translocation of a UV-damaged DNA binding protein into a tight association with chromatin after treatment of mammalian cells with UV light. J. Cell Sci. 110: 1159–1168.
Otrin, V.R., Kuraoka, I., Nardo, T., McLenigan, M., Eker, A.P.M., M. Stefanini, M., Levine, A.S. and Wood, R.D. 1998. Relationship of the xeroderma pigmentosum group E DNA repair defect to the chromatin and DNA binding proteins UV-DDB and replication protein A. Mol. Cellu. Biol. 18: 3182–3190.
Pasheva, E.A., Pashev, I.G. and Favre, A. 1998. Preferential binding of high mobility group I protein to UV-damaged DNA: Role of the COOH-terminal domain. J. Biol. Chem. 273: 24730–24736.
Samuel, A. 2000. Vertebrate evolution: Recent perspectives from fish, Trends Genet. 16: 54–56.
Sancar, G.B. 1990. DNA photolyases: Physical properties, action mechanism and roles in dark repair. Mutat. Res. 236: 147–160.
Seidl, C. and Moritz, K.B. 1998. A novel UV-damaged DNA binding protein emerges during the chromatin-eliminating cleavage period in Ascaris suum, Nucl. Acids Res. 26: 768–777.
Setlow, R.B. 1966. Cyclobutane-type pyrimidine dimers in polynucleotides. Science 153: 379–386.
Szewczuk, Z., Petry, I., Schwanbeck, R. and Renner, U. 1999. Constitutive phosphorylation of the acidic tails of the high mobility group I proteins by casein kinase II alters their conformation, stability, and DNA binding specificity. J. Biol. Chem. 274: 20116–20122.
Tanaka, K., Miura, N., Satokata, I., Miyamoto, I., Yoshida, M.C., Satoh, Y., Kondo, S., Yasui, A., Okayama, H. and Okada, Y. 1990. Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc finger domain. Nature 348: 73–76.
Vichi, P., Coin, F., Renaud, J-P., Vermeulen, W., Hoeijmakers, J.H.J., Moras, D. and Egly, J-M. 1997. Cisplatin-and UVdamaged DNA lure the basal transcription factor TFIID/TBP. EMBO J. 16: 7444–7456.
Wakasugi, M. and Sancar, A. 1998. Assembly, subunit composition, and footprint of human DNA repair excision nuclease. Proc. Natl. Acad. Sci. USA 95: 6669–6674.
Wood, R.D. 1996. DNA repair in eukaryotes. Annu. Rev. Biochem. 65: 135–167.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Hsu, T., Cheng, C., Shih, C. et al. Detection and partial characterization of a UV-damaged-DNA binding activity highly expressed in zebrafish (Danio rerio) embryos. Fish Physiology and Biochemistry 25, 41–51 (2001). https://doi.org/10.1023/A:1019755900858
Issue Date:
DOI: https://doi.org/10.1023/A:1019755900858